@article{18b5416b61934e1b9baf69349aa4886c,
title = "Improved integration of single-cell transcriptome and surface protein expression by LinQ-View",
abstract = "Multimodal advances in single-cell sequencing have enabled the simultaneous quantification of cell surface protein expression alongside unbiased transcriptional profiling. Here, we present LinQ-View, a toolkit designed for multimodal single-cell data visualization and analysis. LinQ-View integrates transcriptional and cell surface protein expression profiling data to reveal more accurate cell heterogeneity and proposes a quantitative metric for cluster purity assessment. Through comparison with existing multimodal methods on multiple public CITE-seq datasets, we demonstrate that LinQ-View efficiently generates accurate cell clusters, especially in CITE-seq data with routine numbers of surface protein features, by preventing variations in a single surface protein feature from affecting results. Finally, we utilized this method to integrate single-cell transcriptional and protein expression data from SARS-CoV-2-infected patients, revealing antigen-specific B cell subsets after infection. Our results suggest LinQ-View could be helpful for multimodal analysis and purity assessment of CITE-seq datasets that target specific cell populations (e.g., B cells).",
keywords = "CITE-seq, computational method, gene expression, integrated model, mRNA, multimodal method, protein, purity metric, scRNA-seq",
author = "Lei Li and Dugan, {Haley L.} and Stamper, {Christopher T.} and Lan, {Linda Yu Ling} and Asby, {Nicholas W.} and Matthew Knight and Olivia Stovicek and Zheng, {Nai Ying} and Madariaga, {Maria Lucia} and Kumaran Shanmugarajah and Jansen, {Maud O.} and Siriruk Changrob and Utset, {Henry A.} and Carole Henry and Christopher Nelson and Jedrzejczak, {Robert P.} and Fremont, {Daved H.} and Andrzej Joachimiak and Florian Krammer and Jun Huang and Khan, {Aly A.} and Wilson, {Patrick C.}",
note = "Funding Information: This project was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH) grants U19AI082724 (P.C.W.), U19AI109946 (P.C.W.), and U19AI057266 (P.C.W.); and NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) grant HHSN272201400005C (P.C.W.). N.W.A. was supported by the Multi-disciplinary Training Program in Cancer Research (MTCR), NIH T32 CA009594 . A.J. and R.P.J. were supported by federal funds from the NIAID, NIH , and Department of Health and Human Services under contract HHSN272201700060C . F.K was funded by NIAID CEIRS contract HHSN272201400008C , Collaborative Influenza Vaccine Innovation Centers (CIVIC) contract 75N93019C00051 , and the generous support of the JPB Foundation , the Open Philanthropy Project (2020-215611), and other philanthropic donations. D.F. and C.N. were supported by NIAID contracts HHSN272201700060C and 75N93019C00062 . We would like to thank Dr. Congting Ye for his assistance and suggestions for this project. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = aug,
day = "23",
doi = "10.1016/j.crmeth.2021.100056",
language = "English",
volume = "1",
journal = "Cell Reports Methods",
issn = "2667-2375",
number = "4",
}